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Oops, I meant to reply all: 

Hi R ,

See below, I gave 8 GB and 2 CPU in settings.




--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego

From: fsbuild@convergenceservice.com <fsbuild@convergenceservice.com>
Sent: Monday, May 9, 2022 2:41 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Joanna L Eckhardt <jeckhardt@health.ucsd.edu>
Subject: Re: [Freesurfer] Recon-all Freezes on Parallel
 
In the VirtualBox settings, did you give the VM both cores to use?

It would also be good to know much memory your machine has, and how much of that you gave to the VM in the VirtualBox settings.

- R.

On May 9, 2022, at 17:27, Joanna L Eckhardt <jeckhardt@health.ucsd.edu> wrote:

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Dear FreeSurfer Team, 

I have been trying to use the parallel command (following FreeSurfer tutorial) to run multiple subjects (Windows os running Ubuntu VM).

I only have 2 cores, so I have it set to 2 jobs instead of 8 as in the tutorial. When I use the code from the tutorial, there is an error with the .nii, and I assume it is because my files are .nii.gz.
developer@developer-VirtualBox:~/FreeSurfer/Cannabis_Reduced$ ls *.nii | parallel --jobs 3 recon-all -s {.} -i {} -all -qcache
ls: cannot access '*.nii': No such file or directory
So I changed the code to .gz with everything else the same, and FreeSurfer does nothing (it stalls/freezes). Is this just because my computer cannot handle the job? Is there anything else I can do to run parallel? If not, I can always just run 1 subject at a time, but I want to check and see if there is another way to get this to work. 

Thank you for your time!
Joanna
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